The Fusarium graminearum species complex (FGSC) is a pathogen of durum wheat and other cereals worldwide. The complex consists of at least 15 species that can produce various mycotoxins, including trichothecenes, associated with human and animals toxicoses. In particular, deoxynivalenol (DON), nivalenol (NIV) and their different acetylated derivatives can be produced by the different chemotypes of the complex. In this study, 90 strains, isolated mainly from wheat in Italy and belonging to the FGSC, were assessed for their phylogeny and their chemotype and trichothecene genotype. Almost all strains of the FGSC belonged to F. graminearum sensu stricto, whereas two strains were F. cortaderiae. On the other hand, all three chemotypes, 3ADON, 15ADON and NIV, occurred; 15ADON was the most common molecular chemotype. The data show that the species composition of the Italian FGSC is homogeneous, whereas wide chemotype variability can occur within F. graminearum sensu stricto.